CSE Citation-Sequence and CSE Citation-Name

In both CSE citation systems described here, numbers in a sentence refer to sources listed at the end of the document. These two systems differ only in how sources are numbered in the reference list: sequentially (citation-sequence) or alphabetically by author’s name (citation-name).

In-text references

Format in-text references

The style advocated by CSE suggests that numbers appear in superscript, and appear before punctuation marks (commas or periods).

Example from The CSE Manual:

Traumatic life events and posttraumatic stress disorder (PTSD) are endemic among American civilians 1.

However, many scientific journals format these numbers differently, using square brackets or parentheses, or putting superscript numbers after the period.

Example from Communicative & Integrative Biology (2011):

The most fundamental specialization of the eusocial insects is the division of colony members into two castes, workers (functionally sterile individuals) and reproductives.1

Example from Current Opinion in Cell Biology (2012):

The classical cadherin system connects cadherins to the actin cytoskeleton via b-catenin and a-catenin to maintain tissue integrity in metazoans [1].

Example from mBio (2012):

Although xylem is considered a nutrient-limiting, low-oxygen environment (1), R. solanacearum is well adapted to it, growing to cell densities of 108 to 109 CFU/g stem while still remaining limited to xylem (2).

For consistency, the examples that follow have been reformatted to match CSE’s preferred style (superscripted numerals before punctuation).

Number in-text references

  • In the citation-sequence system, sources are numbered by order of reference so that the first reference cited in the paper is 1, the second 2, and so on.
  • In citation-name, the sources are numbered alphabetically so that 1 refers to the first source in an alphabetical list, 2 refers to the second source in that list, and so on.

When possible, put numbers immediately after the relevant word or phrase rather than at the end of a sentence.

Cite multiple sources in one sentence

If the numbers are not in a continuous sequence, use commas (with no spaces) between numbers. If you have more than two numbers in a continuous sequence, use the first and last number of the sequence joined by a hyphen.

Example from A new model for caste development in social wasps by UW-Madison Professor Robert Jeanne (Entomology) and postdoc Sainath Suryanarayanan (Community and Environmental Sociology):

For the non-dimorphic polistines such as Polistes, Ropalidia and others, the long-standing view is that differences in the quantity of nourishment received during the larval stage act as a “nutritional switch” to bias development toward one caste or the other 7,8,11-14.

Example from Cadherin complexity: recent insights into cadherin superfamily function in C. elegans by UW-Madison graduate student Timothy Loveless (Cellular and Molecular Biology) and Professor Jeff Hardin (Zoology):

Basolateral foci of HMP-1 and DLG-1 accumulate despite unperturbed localization of LET-413/Scribble 19, which normally excludes AJ components from basolateral surfaces 23,24.

Cite one source in multiple sentences

Once you have assigned a source a number, use that same number every time you cite it.

Example from Contrast Agents for Magnetic Resonance Imaging Synthesized with Ring-Opening Metathesis Polymerization by UW-Madison Biochemistry postdoc Matthew J. Allen and Professors Ronald J. Raines and Laura L. Kiessling:

Moreover, the use of ROMP is advantageous because it can yield polymers of well-defined length 6. To synthesize the target polymers 8a and 8b we employed the ruthenium initiator (H2IMes)(3-Br-py)2(Cl)2RudCHPh. Its rate of initiation relative to propagation affords polymers of well-defined average lengths 6,8.

Example from The Role of Secretion Systems and Small Molecules in Soft-Rot Enterobacteriaceae Pathogenicity by UW-Madison Professor Amy Charkowski (Plant Pathology) et al.

Once associated with an insect, some isolates of Pectobacterium carotovorum can infect and persist in D. melanogaster and activate an immune response 8,9. The protein Evf (Erwinia virulence factor), present only in insect-associated strains, promotes the persistence of bacteria in the insect midgut. Evf synthesis is regulated by SlyA (Hor), which also regulates plant virulence genes 1,9.

Cite sources in tables and figures

Avoid using superscripted numerals in figures where they might be misconstrued as exponents. Instead, use superscripted letters like a,b for tables and figures. List them sequentially after all the text citations.

Quote or excerpt a source

Although CSE provides rules for how to quote or excerpt sources, in practice almost no scientists publishing in journals that use CSE documentation choose to quote sources. Instead, these authors paraphrase or simply cite authors.

When you quote or excerpt a source, include an in-text reference to help your reader see what source you are quoting from. The seventh edition of the CSE Manual does not provide specific rules for identifying the page number or other location information for that source.

Cite a work cited by your source (secondary citation)

Secondary citations refer to material that you have not seen in its original form but rather have obtained from another document that cited the original source. In the 2006 edition of the CSE Manual, secondary citations are not listed as a valid form of citation. Instead, find and cite the original source.

End references and the reference list

The goal of your reference list is to help your reader identify each numbered source quickly and clearly. CSE has standardized the information to be provided for ease and predictability of reading.

What to call your reference list

“Reference list” is CSE’s generic term for the list of sources at the end of your document. Your list should be given a more formal title: References or Cited References. If you used some documents as sources but did not cite them in your paper, list them alphabetically by author under the heading Additional References.

Format your end references

  • Authors’ first names are rendered as capitals after their surnames.

    Otegui MS, Kiessling LL, Batzli J.

  • Only the first word of a book or article title should be capitalized.

    The fat-soluble vitamins: handbook of lipid research 2.

  • Titles are not italicized. However, species names are italicized.

    In vitro and in vivo reconstitution of the cadherin-catenin-actin complex from Caenorhabditis elegans. Proc Natl Acad Sci. 2010 Aug 17;107(33):14591-6.

  • To save space, journal titles are abbreviated according to the ISO 4 standard, shortening significant words and omitting insignificant words. Read more and search the List of Title Word Abbreviations at ISSN.org.

    Livestock Prod Sci.
    Biochem Mol Biol Educ.
    J Dairy Sci.

  • Year of publication and volume number are required for all references to articles. Issue number is strongly recommended. To save space, use no spaces to separate an article’s date, volume, and page.

    Annu Rev Phytopathol. 2012;50:425-49. Mol Plant Microbe Interact. 2011 Jul;24(7):773-86.

Examples of end references


References for books follow the order Author(s). Title. Edition. Place of publication: publisher; date. Extent.

1 Allen C, Prior P, Hayward AC. Bacterial wilt: the disease and the Ralstonia solanacearum species complex. St. Paul (MN): APS Press; 2005. 508 p.

[A book’s extent in number of pages (“508 p.” in the example above) is optional but provides useful information.]

Book chapter

References for chapters or other parts of a book follow the order Author(s). Chapter title. In: Editor(s). Book title. Place of publication: publisher; year. Page numbers for that chapter.

2 Otegui MS. Endosperm: development and molecular biology. In: Olson OA, editor. Endosperm cell walls: formation, composition, and functions. Heidelberg (Germany): Springer-Verlag; 2007. p. 159-178.

3 Allen, C. Bacteria, bioterrorism, and the geranium ladies of Guatemala. In: Cabezas AL, Reese E, Waller M, editors. Wages of empire: neoliberal policies, repression, and women’s poverty. Boulder (CO): Paradigm Press; 2007. p. 169-177.

Journal article

References for journal articles follow the order Author(s). Article title. Abbreviated journal title. Date;volume(issue):pages.

To save space, CSE suggests that writers abbreviate the titles of journals in according to the ISO 4 standard, which you can read about at ISSN. You can also search ISSN’s List of Title Word Abbreviations.

4 Wang Y, Zhu J, DeLuca HF. Where is the vitamin D receptor? Arch Biochem Biophys. 2012 Jul 1;523(1):123-33.

5 Powell JM, Wattiaux MA, Broderick GA. Evaluation of milk urea nitrogen as a management tool to reduce ammonia emissions from dairy farms. J Dairy Sci. 2011;94(9):4690-4694

6 Flores-Cruz Z, Allen C. Necessity of OxyR for the hydrogen peroxide stress response and full virulence in Ralstonia solanacearum. Appl Environ Microbiol. 2011;77(18):6426-6432.

Reference list information for articles found online adds a medium designator—[Internet], including the brackets—at the end of the title of the journal, as well as a citation date and a URL. The CSE Manual does not explicitly require this information if the online content is identical to the print content.

7 Werling BP, Lowenstein DM, Straub CS, Gratton C. Multi-predator effects produced by functionally distinct species vary with prey density. J Insect Sci [Internet]. 2012 [cited 12 Sep 2013]; 12(30). Available from: insectscience.org/12.30

8 Bennett AB, Gratton C. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition. Ecol Appl [Internet]. 2013 [cited 12 Sep 2013];23(1):86-95. Available from: http://labs.russell.wisc.edu/gratton/files/2013/03/Ecological-Applications.pdf

Internet resource

9 Williamson RC. Deciduous tree galls [Internet]. Madison (WI): University of Wisconsin-Madison; 2004 Apr 25 [cited 2013 Sep 12]. Available from http://labs.russell.wisc.edu/pddc/files/Fact_Sheets/FC_PDF/Deciduous_Tree_Galls.pdf

10 ASAP: systematic annotation package for community analysis of genomes [Internet]. Madison (WI): University of Wisconsin-Madison; c2013 [cited 2013 Sep 12]. Available from http://www.genome.wisc.edu/tools/asap.htm

11 Stem Cell Research Oversight Committee. University of Wisconsin-Madison policy for multisite research studies using human pluripotent stem cells [Internet]. Madison (WI): University of Wisconsin-Madison; 2009 [cited 2013 Sep 12]. Available from http://www.grad.wisc.edu/admin/committees/scro/documents/MultisiteresearchpolicyFinal.pdf

Government document

12 Working Group on Diversity in the Biomedical Research Workforce (US). Draft report diversity in the biomedical research workforce [Internet]. Bethesda (MD): National Institutes of Health (US); 2012 Jun 13 [cited 2013 Sep 12]. Available from http://acd.od.nih.gov/Diversity%20in%20the%20Biomedical%20Research%20Workforce%20Report.pdf


13 Oliver SS. Context dependent protein interpretation of the histone language [dissertation]. University of Wisconsin-Madison; 2012. 238 p.

Conference presentation or lecture

If a conference paper is subsequently published, either in the proceedings of the conference or in a journal, cite as a chapter in a book or as an article in a journal. Otherwise, cite as follows.

14 Vierstra R. Atomic perspectives on phytochrome photoactivation and signaling. Paper presented at: Steenbock 35. Proceedings of the 35th Steenbock Symposium on Advances in Biomolecular NMR; 2011 June 26-28; Madison, WI.

References for this page

Formatted in Citation-Name style. All examples on this page are taken from publications by UW-Madison professors, postdocs, and graduate students. Note that CSE doesn’t call for hyperlinks.

1 Allen C, Bent A, Charkowski AO. Underexplored niches in research on plant pathogenic bacteria. Plant Physiol [Internet]. [Cited 20 June 2013.] 2009;150(4):1631-1637. Available from http://www.plantphysiol.org/content/150/4/1631.full

2 Bennett AB, Gratton C. Measuring natural pest suppression at different spatial scales affects the importance of local variables. Environ Entomol. 2012;41(5):1077-85.

3 Bennett AB, Gratton C. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition. Ecol Appl. 2013;23(1):86-95.

4 Charkowski A, Blanco C, Condemine G, Expert D, Franza T, Hayes C, Hugouvieux-Cotte-Pattat N, Lopez Solanilla E, Low D, Moleleki L, et al. The role of secretion systems and small molecules in soft-rot enterobacteriaceae pathogenicity. Annu Rev Phytopathol. 2012;50:425-49.

5 Dreyer J, Hoekman D, Gratton C. Lake-derived midges increase abundance of shoreline terrestrial arthropods via multiple trophic pathways. Oikos [Internet]. [Cited 20 June 2013.] 2012;121:252-258. Available from http://labs.russell.wisc.edu/gratton/files/2012/04/Dreyer-et-al.-2012-Lake%E2%80%90derived-midges-increase-abundance-of-shorelin.pdf

6 Gratton C, Vander Zanden MJ. Flux of aquatic insect productivity to land: comparison of lentic and lotic ecosystems. Ecology 2009;90(10):2689-2699.

7 Lyon A, Bell MM, Croll NS, Jackson R, Gratton C. Maculate conceptions: power, process, and creativity in participatory research. Rural Sociology [Internet]. 2010 [cited 20 Jun 2013];75(4):538-559. Available from http://labs.russell.wisc.edu/gratton/files/2012/01/Lyons-et-al-2010-Rural-Soc-Maculate-conceptions.pdf

8 Lyon A, Bell MM, Gratton C, Jackson R. Farming without a recipe: Wisconsin graziers and new directions for agricultural science. J Rural St [Internet]. 2011 [cited 20 June 2013];27:384-393. Available from http://labs.russell.wisc.edu/gratton/files/2012/01/Lyon_Farmingworecipe2011.pdf

9 Mattupalli C, Genger RK, Charkowski AO. Evaluating incidence of Helminthosporium solani and Colletotrichum coccodes on asymptomatic organic potatoes and screening potato lines for resistance to silver scurf. Am J Potato Res [Internet]. 2013 [cited 20 June 2013]. Available from http://link.springer.com/content/pdf/10.1007%2Fs12230-013-9314-3.pdf

10 Thomas DL. Utilization and potential of estimates of genetic value from an industry perspective. Sheep & Goat [Internet]. 2012;27:13-15. Available from http://www.sheepusa.org/user_files/file_1014.pdf

11 Wang Y, DeLuca HF. Is the vitamin d receptor found in muscle? Endocrinology. 2011;152(2):354-63.

12 Wang Y, Borchert ML, Deluca HF. Identification of the vitamin D receptor in various cells of the mouse kidney. Kidney Int. 2012;81(10):993-1001.

13 Wang Y, Marling SJ, Zhu JG, Severson KS, DeLuca HF. Development of experimental autoimmune encephalomyelitis (EAE) in mice requires vitamin D and the vitamin D receptor. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8501-4.

14 Wang Y, Zhu J, DeLuca HF. Where is the vitamin D receptor? Arch Biochem Biophys. 2012;523(1):123-33.

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